Identifying currents in the gene pool for bacterial populations using an integrative approach.

The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relativel...

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Autores principales:	Jing Tang, William P Hanage, Christophe Fraser, Jukka Corander
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/be681b7a55ec4ca7abd7914d4fb11355
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spelling	oai:doaj.org-article:be681b7a55ec4ca7abd7914d4fb113552021-11-25T05:42:15ZIdentifying currents in the gene pool for bacterial populations using an integrative approach.1553-734X1553-735810.1371/journal.pcbi.1000455https://doaj.org/article/be681b7a55ec4ca7abd7914d4fb113552009-08-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19662158/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to the strains. However, the traditional statistical methods for evolutionary inference, such as phylogenetic analysis, are associated with several difficulties under such an extensive sampling scenario, in particular when a considerable amount of recombination is anticipated to have taken place. To meet the needs of large-scale analyses of population structure for bacteria, we introduce here several statistical tools for the detection and representation of recombination between populations. Also, we introduce a model-based description of the shape of a population in sequence space, in terms of its molecular variability and affinity towards other populations. Extensive real data from the genus Neisseria are utilized to demonstrate the potential of an approach where these population genetic tools are combined with an phylogenetic analysis. The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html.Jing TangWilliam P HanageChristophe FraserJukka CoranderPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 5, Iss 8, p e1000455 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Jing Tang William P Hanage Christophe Fraser Jukka Corander Identifying currents in the gene pool for bacterial populations using an integrative approach.
description	The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to the strains. However, the traditional statistical methods for evolutionary inference, such as phylogenetic analysis, are associated with several difficulties under such an extensive sampling scenario, in particular when a considerable amount of recombination is anticipated to have taken place. To meet the needs of large-scale analyses of population structure for bacteria, we introduce here several statistical tools for the detection and representation of recombination between populations. Also, we introduce a model-based description of the shape of a population in sequence space, in terms of its molecular variability and affinity towards other populations. Extensive real data from the genus Neisseria are utilized to demonstrate the potential of an approach where these population genetic tools are combined with an phylogenetic analysis. The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html.
format	article
author	Jing Tang William P Hanage Christophe Fraser Jukka Corander
author_facet	Jing Tang William P Hanage Christophe Fraser Jukka Corander
author_sort	Jing Tang
title	Identifying currents in the gene pool for bacterial populations using an integrative approach.
title_short	Identifying currents in the gene pool for bacterial populations using an integrative approach.
title_full	Identifying currents in the gene pool for bacterial populations using an integrative approach.
title_fullStr	Identifying currents in the gene pool for bacterial populations using an integrative approach.
title_full_unstemmed	Identifying currents in the gene pool for bacterial populations using an integrative approach.
title_sort	identifying currents in the gene pool for bacterial populations using an integrative approach.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/be681b7a55ec4ca7abd7914d4fb11355
work_keys_str_mv	AT jingtang identifyingcurrentsinthegenepoolforbacterialpopulationsusinganintegrativeapproach AT williamphanage identifyingcurrentsinthegenepoolforbacterialpopulationsusinganintegrativeapproach AT christophefraser identifyingcurrentsinthegenepoolforbacterialpopulationsusinganintegrativeapproach AT jukkacorander identifyingcurrentsinthegenepoolforbacterialpopulationsusinganintegrativeapproach
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Identifying currents in the gene pool for bacterial populations using an integrative approach.

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